Examining the multi-species impact on the built-space microbiome of a small-scale USDA inspected animal processing facility

Abstract

The global population continues to expand, driving a need for increased food production, including animal-derived proteins from poultry, pork, beef, and lamb. In the US, large-scale processing facilities dominate the meat industry; however, there is intense interest in expanding access to small, community-based multi-species meat processing facilities to meet local producer and consumer needs. Small-scale multi-species meat processing facilities face unique challenges that pose additional food safety risks due to potential cross-species contamination. Whether a USDA-mandated one-size-fits-all food safety plan adequately prevents cross-species contaminations remains unclear. Another uncertainty is the degree multi-species processing impacts the inherent microbiota throughout a facility from live animal to cooked product. To address this, we investigated the longitudinal microbiota profile of the newly built Meat Science & Animal Biologics Discovery Building USDA-inspected processing facility and the effects of multi-species processing on the built-space microbiota community of 10 key locations in the facility. I hypothesize that microbiome communities will establish themselves as comparatively different from that of the initial baseline microbiome and, unique, predictable, shifts will be observed at key facility locations following the processing of each species (beef and pork). To address this, baseline swabs of the facility, prior to any animal harvests in 2020, were collected using 3MTM sponge-stick swabs with 10mL buffered peptone water. Re-sampling was performed at 10 “high-touch” locations (animal holding pens, drains, facility doors, and production areas) for an intermediate baseline in 2023 and between each species 24 – 48-hours after harvest and sanitation procedures were completed. Genomic DNA was extracted directly from the swabs using Qiagen Powersoil Pro Max kits, and community membership assessed via next-generation Illumina MiSeq for 16S rRNA amplicon sequencing of the V4 region followed by QIIME2-2022.2 analysis using the DADA2 pipeline. We observed that drain swabs exhibited increased alpha-diversity assessed via Pielou’s evenness and number of observed species relative to all other facility locations (P<0.05). When looking at the true baseline and intermediate baseline of the facility, there was notable variations in alpha-diversity across swab sites, unexpected decreases in observed species at drain locations, and a stable microbial population at many swab sites from 2020 to 2023. Additionally, the analysis of specific taxa highlights a heightened presence of Pseudomonas in 2023, calling for considerations in safety and sanitation protocols in multi-species processing facility. Further, beta-diversity analysis of both weighted and unweighted UniFrac distances analyzed by Wilcoxon Rank-Sum Test revealed the beef hide swab microbiota were different from microbes observed on swabs from all other facility locations (P<0.05). Similar, yet more robust, differences were observed between pig skin swabs and swabs from all other facility locations (P<0.0001). The robust differences in facility vs. pig skin UniFrac distances as compared to those observed between facility and beef hide suggest the facility's microbiota community membership aligns more closely to beef despite multi-species processing. Our findings provide a framework for monitoring selective pressures of multi-species processing and identifying best sanitation practices that will mitigate food safety concerns with multi-species contamination.